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Maintenance of tolerance after lung transplantation is dependent on the preservation of allograft tissue-resident Foxp3+ T cells

GSE251931 Mus musculus (mouse) Single-cell RNA-seq 15 samples Submitted 2025/05/22 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 15 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
15 samples: 15 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Maintenance of graft tissue-resident Foxp3+ cells is necessary for lung transplant tolerance in miceThe Journal of clinical investigation · 2025
Summary (written by the submitters)
Mechanisms of allograft tolerance differ between organs. We have previously shown that Foxp3+ T cell (Treg)-enriched bronchus-associated lymphoid tissue is induced in tolerant murine lung allografts and that graft-resident Tregs suppress B cell activation to maintain tolerance. Here, using our previously described retransplant model, we examined whether continuous recruitment of Tregs to the allograft is required to maintain tolerance.
Read the full summary ↓
We found that graft-infiltrating Tregs migrate to BALT where they interact with graft-resident CD11c+ and Foxp3+ cells. Graft-infiltrating and graft-resident Tregs are likely of thymic origin but have different gene expression profiles at the single cell level. Following retransplantation of a tolerized left lung graft into a non-immunosuppressed B6.Foxp3-DTR secondary recipient, we depleted graft-infiltrating Tregs by administering diphtheria toxin. When graft-infiltrating Tregs are depleted, the lung allograft has gross and histological evidence of rejection and is associated with B cell activation and development of donor-specific alloantibodies in the serum. These phenotypes are rescued when B cell-depleting anti-CD20 antibody is administered, further supporting an antibody-mediated mechanism by which graft-infiltrating Tregs maintain tolerance. Finally, we show that recombinant IL-33 administration can be used to expand the Treg population following murine lung transplant.
Published in
Maintenance of graft tissue-resident Foxp3+ cells is necessary for lung transplant tolerance in mice
Li W, Terada Y, Bai YZ et al. · The Journal of clinical investigation 2025 · PMID 40100295 · doi:10.1172/JCI178975
This dataset
Open GSE251931 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE251931_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1055942 and SRA study SRP479705. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40100295) ↗
Study design
15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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